GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgD in Acidovorax sp. GW101-3H11

Align 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) (characterized)
to candidate Ac3H11_2339 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41)

Query= BRENDA::B7WZA5
         (303 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2339
          Length = 303

 Score =  536 bits (1382), Expect = e-157
 Identities = 264/303 (87%), Positives = 278/303 (91%)

Query: 1   MTPQDLKDVMSSGLLSFPVTDFDAQGNFNAKGYAARLEWLAPYGASALFAAGGTGEYFSL 60
           MTPQDLK +M SGLLSFP+TDFD QGNF  K Y  RLEWLAPYGASALFAAGGTGEYFSL
Sbjct: 1   MTPQDLKTIMGSGLLSFPITDFDEQGNFRPKTYIERLEWLAPYGASALFAAGGTGEYFSL 60

Query: 61  YGEEYGQIIKTAVDTCRGKVPIIAGAGGPTRTAIAHAQEAERLGAHGILLLPHYLTEAGQ 120
            G EY ++IKTAVDTCRGKVPIIAGAGGPTRTAIAHAQEAERLGAHGILLLPHYLTEAGQ
Sbjct: 61  SGPEYSEVIKTAVDTCRGKVPIIAGAGGPTRTAIAHAQEAERLGAHGILLLPHYLTEAGQ 120

Query: 121 EGLIAHVEQVCKSVKFGVIVYNRDRTRFTPESLAILAERCPNLVGFKDGMGNIETMSSIF 180
           EGLI HV QVC SVKFGVIVYNRDRT+ T ESLAILAERCPNL+GFKDG+GNIETMSSI+
Sbjct: 121 EGLIEHVAQVCNSVKFGVIVYNRDRTKLTAESLAILAERCPNLIGFKDGVGNIETMSSIY 180

Query: 181 MKMGDRFAYLGGLPTAEVYAAAYKALGTPVYSSAVFNFIPRTAMAFYEAVRTDDMATQHK 240
           MKMGDRF+YLGGLPTAEVYAAAYKALGTPVYSSAVFNFIP+TAM FY+AV  DD+ATQHK
Sbjct: 181 MKMGDRFSYLGGLPTAEVYAAAYKALGTPVYSSAVFNFIPKTAMDFYKAVAADDIATQHK 240

Query: 241 LLKEFFMPYLKIRNRVEGYGVSIIKAGAKLVGHDAGPVRAPLTDLKPAEMEELKVLIDKL 300
           LLKEFFMPYL IRNRVEGYGVSIIKAGAK+VGHD GPVRAPLTDLKP E+EEL  LI KL
Sbjct: 241 LLKEFFMPYLAIRNRVEGYGVSIIKAGAKIVGHDGGPVRAPLTDLKPHEVEELAALIKKL 300

Query: 301 GPQ 303
           GPQ
Sbjct: 301 GPQ 303


Lambda     K      H
   0.320    0.138    0.405 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 447
Number of extensions: 9
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 303
Length of database: 303
Length adjustment: 27
Effective length of query: 276
Effective length of database: 276
Effective search space:    76176
Effective search space used:    76176
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate Ac3H11_2339 (5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41))
to HMM TIGR03249 (kdgD: 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41))

Software error:

../bin/blast/fastacmd -i /tmp/list.31378.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.31378.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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